KCsmart (version 2.30.0)

write.table: Write summary of the significant regions to a table

Description

Write summary of the significant regions to a table

Usage

write.table(x, file = "", append = FALSE, quote = TRUE, sep = " ", eol = "\n", na = "NA", dec = ".", row.names = TRUE, col.names = TRUE, qmethod = c("escape", "double"), fileEncoding = "")
"write.table"(x, file="", append = FALSE, quote = 7, sep = "\t", eol = "\n", na = "NA", dec = ".", row.names = TRUE, col.names=c("Status", "Chromosome", "Start", "End", "Average KC score", "Mode KC score", "Probes"), qmethod = c("escape", "double"))
"write.table"(x, file="", append = FALSE, quote = 7, sep = "\t", eol = "\n", na = "NA", dec = ".", row.names = FALSE, col.names=c("startrow", "endrow", "chromosome", "startposition", "endposition"), qmethod = c("escape", "double"))

Arguments

x

The sigSegments object to be summarized

file

either a character string naming a file or a connection open for writing. '""' indicates output to the console.

append

logical. Only relevant if 'file' is a character string. If 'TRUE', the output is appended to the file. If 'FALSE', any existing file of the name is destroyed.

quote

a logical value ('TRUE' or 'FALSE') or a numeric vector. If 'TRUE', any character or factor columns will be surrounded by double quotes. If a numeric vector, its elements are taken as the indices of columns to quote. In both cases, row and column names are quoted if they are written. If 'FALSE', nothing is quoted.

sep

the field separator string. Values within each row of 'x' are separated by this string.

eol

the character(s) to print at the end of each line (row).

na

the string to use for missing values in the data.

dec

the string to use for decimal points in numeric or complex columns: must be a single character.

row.names

either a logical value indicating whether the row names of 'x' are to be written along with 'x', or a character vector of row names to be written.

col.names

either a logical value indicating whether the column names of 'x' are to be written along with 'x', or a character vector of column names to be written. See the section on 'CSV files' for the meaning of 'col.names = NA'.

qmethod

a character string specifying how to deal with embedded double quote characters when quoting strings. Must be one of '"escape"' (default), in which case the quote character is escaped in C style by a backslash, or '"double"', in which case it is doubled. You can specify just the initial letter.

fileEncoding

character string: if non-empty declares the encoding to be used on a file (not a connection) so the character data can be re-encoded as they are written. See file.

Details

Writes a summary of the sigSegments object to file. The resulting table contains 7 columns. The interpretation of the columns is as follows:

• Status Either 'L' for loss or 'G' for gain
• Chromosome The chromosome on which this segment is located
• Start The start position (in base pairs) of the segment on the chromosome
• End The end position of the segment on the chromosome
• Average KC scoreThe average KCsmart score over all base pairs in this segment
• Mode KC scoreThe highest (for gains) or lowest (for losses) KCsmart score over all base pairs in this segment
• Probes All probes from the original data that fall into this segment

See Also

calcSpm, getSigSegments

Examples

data(hsSampleData)
data(hsMirrorLocs)

spm1mb <- calcSpm(hsSampleData, hsMirrorLocs)

siglevel1mb <- findSigLevelTrad(hsSampleData, spm1mb, n=3)

sigSegments1mb <- getSigSegments(spm1mb, siglevel1mb)
write.table(sigSegments1mb, file=file.path(tempdir(),'sigSegments1mb.txt'))